Dear all,

I have a set of T1-MPRAGE images and and conducted the following steps:

1- Converted the DICOM images to SPM8 (3D nifti nii) by dcm2niigui.exe

2- Used the following line to segment images by FreeSurfer:

recon-all -i /xxx/IM-0009-0001.dcm -subject TEST -all

recon-all -base TESTBASE -tp TEST -all

recon-all -long TEST TESTBASE -all

3- Used FSL BET to skull strip the nii file from step 1 and then fed the output into FSL FAST segmentation to segment it to 3 classes.

4- Used the following line to convert the mgz file to nii

mri_convert --in_type mgz --out_type nii --out_orientation RAS /xxx/mri/brainmask.mgz /xxx/test_brainmask.nii

5- Using the fslinfo it gives me the following info for test_brain.nii.gz

data_type FLOAT32

dim1 192

dim2 240

dim3 256

dim4 1

datatype 16

pixdim1 1.000000

pixdim2 1.000000

pixdim3 1.000000

pixdim4 1.000000

cal_max 0.0000

cal_min 0.0000

file_type NIFTI-1+

while for the nii file from step 4 the fslinfo gives me:

data_type UINT8

dim1 256

dim2 256

dim3 256

dim4 1

datatype 2

pixdim1 1.000000

pixdim2 1.000000

pixdim3 1.000000

pixdim4 2.300000

cal_max 0.0000

cal_min 0.0000

file_type NIFTI-1+

As you may see these two files are completly different so I am not able to overlay them using FSLVIEW. Any idea about how to overlay them ?

Thank you,

Mahmoud